The Albert Einstein Cancer Center has been in the forefront of development of technologies for the analysis of gene expression, beginning with the first large scale gene array and image analysis systems developed over a decade ago, and continuing to high throughput genomics facilities for microarray analysis, mapping and sequencing, and novel technologies for quantitative in situ analysis of multiple mRNA molecules at single molecule resolution and sensitivity. An integrated program utilizing these technologies is presented that focuses on identifying subsets of Dukes' B2 and C colon cancer patients, an area of basic and clinical research in which we have been active throughout this decade. Approximately 50,000 patients per year will have adjuvant chemotherapy recommended following resection, and there is a critical need to distinguish subsets who will benefit from this treatment from subsets who either do not require further treatment, or who will not benefit, and should be spared the expense and toxicity of treatment, The latter patients with poor prognosis would also be candidates for more aggressive treatment, including gene therapy. Patients will be identified and tissue obtained through a collaborative program among the Departments of Surgery, Pathology and Oncology for capturing and following patients on clinical trials. A unique feature of our application is our development and analysis of extensive microarray databases on lineage specific differentiation of colonic epithelial cells both accompanied by, or independent of, apoptotic pathways, and our microarray analysis of isogenic colonic cell lines that over-express c-myc mRNA and protein to differing degrees. These in vitro data provide biological rationales which will help guide analyses of the in vivo data. In addition to fully operational facilities, other unique features of our program include the use of Real Time PCR for microarray calibration and quality control, and analysis of tissue obtained by laser capture microscopy; linkage to major programs in structural genomics and development and analysis of novel mouse models of colon cancer; an in place bioinformatics program which services the genomics and genetics programs of the Cancer Center; the collaboration of a biostatistics group with extensive experience in basic and translational research for the planning and analysis of the experiments; and a resource of banked normal and tumor DNA from over 700 patients entered into 2 phase III studies of adjuvant therapy for colon cancer, including the last multi- institutional study for which there is a control arm for analysis of the natural history of the disease, which will permit rigorous analysis of structural gene alterations that may underlie alterations in expression.